Thanks for your help. Somehow this was the way it was copied into
users home directories, but was correct in the fsl directories.
Do you know what command may have altered it for future reference?
Thanks,
Diana
This is what it was previously:
qform_name Unknown
qform_code 0
qto_xyz:1 2.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 2.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 2.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Aligned Anat
sform_code 2
sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL3.2beta
aux_file none
On Sep 28, 2007, at 3:07 AM, Mark Jenkinson wrote:
> Hi,
>
> All the sform and qform fields for avg152T1_brain.nii.gz are
> exactly the
> same when I look at them. I've attached the relevant bits of fslhd
> below.
> What do you get?
>
> We generally write out both qform and sform to be identical except
> where
> they are initially set-up separately. The reason there are two
> fields is
> that qform was originally intended to store the scanner orientation
> (like
> that found in the dicom) and sform was intended to store standard-
> space
> information. In order to be the most compatible with other
> software, at
> present, we set them to be equal whenever possible (noting that the
> sform
> can store 12 dof transforms, but the qform can only store 6 dof ones).
>
> If you are seeing different values in your standard images, then it
> sounds
> like they may have been corrupted.
>
> All the best,
> Mark
>
>
> % fslhd /usr/local/fsl/data/standard/avg152T1_brain.nii.gz
> ....
> qform_name MNI_152
> qform_code 4
> qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
> qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
> qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name MNI_152
> sform_code 4
> sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
> sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
> sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
>
>
>
>
> On 27 Sep 2007, at 17:05, Diana Wallin wrote:
>
>> Hi,
>>
>> Can someone explain to me the difference between qform_xorient,
>> _yorient, _zorient and sform_xorient, _yorient, and _zorient?
>>
>> I'm confused as to why qform and sform differ in the xorient in
>> the standard brain (avg152T1_brain.nii.gz), but in the data I am
>> analyzing, both fields are always identical.
>>
>> Thanks in advance,
>> Diana
>>
>>
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>
>
> The information transmitted in this electronic communication is
> intended only for the person or entity to whom it is addressed and
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> retransmission, dissemination or other use of or taking of any
> action in reliance upon this information by persons or entities
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> this information in error, please contact the Compliance HelpLine
> at 800-856-1983 and properly dispose of this information.
>
The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information.
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